DNA BASED COMPUTER
Authors:
M.Balaji & T.Ashok kumar
IT (III) year.
Sri Venkateswara College of Engineering &Technology
Thiruvallur-631203
M.Balaji
S/o G.Mahadevan
No: 10,Purananuru street, Sri Sakthi Nagar,
RCC Post, Chennai-600109.
Contact number: 9566192992
Email:balaji_620@yahoo.co.in
ABSTRACT
“Everything looks good when it is mounted on a chip.”
The area of bio-molecular computing has recently
witnessed a major paradigm shift. Rather than being used only
as simple calculating units capable of solving hard combinatorial
or numerical problems, DNA computers are increasingly
becoming more tailored to operate like intelligent biological
machines with unprecedented potentials. One example of
applying DNA computers in such a new setting is in the area of
logical control of gene expression levels. For this purpose, DNA
computers are designed in such away as to be able to diagnose
some forms of cancer-related irregularities in a cell and release
biological strands acting as inhibitors or activators of certain sets
of genes. Such a control action can also be seen as a form of
intra-cell cancer therapy, although it may also have other, more
varied, purposes and goals. There are several important
problems in the area of coding and network theory that arise in
the context of developing DNA computers for controlling gene
expressions. The two most important issues are that of
minimizing diagnostics failure and of increasing the
computational reliability of the system. The first question is
intimately related to analyzing the operational principles of
networks of gene interactions, while the second is concerned with
relating combinatorial characteristics of single stranded DNA
sequences to their hybridization affinities and secondary
structures. In this paper, we will describe the state-of-the-art
results and present some new relevant combinatorial and coding
theoretic problems in this area.
INTRODUCTION TO DNA COMPUTER
Computer chip manufactures are furiously racing to
make the next microprocessor that will topple speed records.
Sooner or later, though, this competition is bound to hit a wall.
Microprocessor made of silicon will eventually reach their
limits of speed and miniaturization. Chip makers need a new
material to produce faster computing speeds.
T.Ashok kumar
S/o S.Thangaraj
No: 3, 3rd street,Bharathi Nagar,
Thirumullaivoyal, Chennai-600062.
Contact number: 9884202521
Email:ashok.tiger@gmail.com
You won’t believe where scientists have found the new
material they need to build the next generation of
microprocessors. Millions of natural supercomputers exist
inside living organisms, including your living body. DNA
(deoxyribonucleic acid) molecules, the material our genes are
made of, have the potential to perform calculations many
faster than the world’s most powerful human-built computers.
What is a DNA Computer?
Research in the development of DNA computers is really
only at its beginning stages, so a specific answer isn't yet
available. But the general sense of such a computational
device is to use the DNA molecule as a model for its
construction. Although the feasibility of molecular computers
remains in doubt, the field has opened new horizons and
important new research problems, both for computer scientists
and biologists. The computer scientist and mathematician are
looking for new models of computation to replace with acting
in a test tube.
HAMILTON PATH PROBLEM
Adelman is often called the inventor of the DNA
computers. His article in a 1994 issue of Journal Science
outlined how to use DNA to solve a well-known mathematical
problem, called the “Directed Hamilton Path problem”, also
known as the “Traveling Salesman Problem”. The goal of the
problem is to find the shortest route between a numbers of
cities, going through each city only once. As you add more
cities the problem becomes more difficult.
 The two helices are joined by “bases”, which will be
represented by colored blocks. Each base binds only
to one other specific base. In our example, we will
say that each colored block will bind only with the
block of same color. For example, if we

Figure shows a diagram of the Hamilton path problem.

The objective is to find a path from start to end going through only had red colored blocks, they would form a long
all the points only once. This problem is difficult for the chain like this:
conventional (serial logic) computers because they try must
try each path one at a time. It is like having a whole bunch of
Any other colors will not bind with red:
keys and trying to see which fits into the lock. Conventional
computers are very good at math, but poor at “key into lock”
problems. DNA based computers can try all the keys at the
same time (massively parallel) and thus are very good at key
into lock problems, but much slower at simple mathematical
problems like multiplication. The Hamilton path problem was
chosen because every key-into-lock problem can be solved as
a Hamilton Path Problem. Figure showing the possible flight
routes between the seven cities.
PROGRAMMING OF THE PROBLEM USING DNA

The following algorithm solves the Hamilton Path Problem,

regardless of the type computers used.
1. Generate random paths through the graph.
STEP 1: Create a unique DNA sequence for each city A
through G. For each path, for example, from A to B, creates
a linking pieces of DNA that matches the last half of A and
first half of B:

2. Keep only those paths that begin with the start city
(A) and conclude with the end city (G).

3. Because the graph has 7 cities, keep only those

paths with 7 cities. Here the red block represents the city a, while the orange
block represents the city B. the half-red half-orange block
4. Keep only those paths that enter all cities at least connecting the two other blocks represents the path from A to
once. B.

5. Any remaining paths are solutions.
The key to solving the problem was using DNA to
perform the five steps in solving the above
algorithm.
These interconnecting blocks can be used to model DNA:
In a test tube, all different pieces of DNA will randomly link
with each other, forming paths through the graph.
STEP 2: Because it is difficult to "remove" DNA from
solution, the target DNA, the DNA which started from A and
ended at G was copied over and over again until the test tube
contained a lot of it relative to other random sequences. This
is essentially the same as removing all the other pieces.
Imagine a sock drawer which initially contains one or two
coloured socks. If you put in a hundred black socks, the
chances are that all you will get if you reach in is black
socks.

DNA likes to form long double helices:

STEP 3: Going by weight, the DNA sequences which were 7
"cities" long were separated from the rest. A "sieve" was used
which would allow smaller pieces of DNA to pass quickly,
while larger segments are slowed down. the procedure used
actually allows you to isolate the pieces which are precisely 7
cities long from any shorter or longer paths.
STEP 4: To ensure that the remaining sequences went
through each of cities, “sticky” pieces of DNA attached to
magnets were used to separate the DNA. The magnets were
used to ensure that the target DNA remained in the test tube,
while the unwanted DNA was washed away. First, the
magnets kept all the DNA which went through city A in the
test tube, then B, then C, and D, and so on. In the end, the
only DNA which remained in the tube was that which went
through all seven cities.
STEP 5: all that was left to sequences the DNA,
revealing the path from A to B to C to D to E to F to G.
FIRST DNA COMPUTER
Olympus Optical Co., Ltd. (President Tsuyoshi
Kikukawa) has announced the successful development of the
world's first functional DNA computer for gene analysis, an
area with enormous projected research- and analysis-related
demand.
APPLICATIONS OF FIRST GENERATION DNA
COMPUTERS
• Gene analysis.
• Useful to Government to break secret codes
• To Airlines to map efficient routes
• To understand about human Brain – the natural Super
Computer
CONSTRUCTION OF DNA COMPUTER FOR GENE ANALYSIS
The computer has a hybrid form and consists of two
sections (molecular and electronic), both of which
perform computational calculations. This distribution
of computational functions helps to raise the overall
speed of the process.
• Artificial DNA fragment, designed by using special
software which has special property physicochemical
that make up memory.
• Allows scientist to observe chemical reaction.
• Start gene analysis using the DNA computer on trial
basis for a year.
ADVANTAGES
• Perform millions of operations simultaneously.
• Generate a complete set of potential solutions.
Conduct large parallel searches.
• Efficiently handle massive amounts of working
memory.
• As long as there are cellular organisms, there will
always be a supply of DNA.
• The large supply of DNA makes it a cheap resource.
• DNA computers are many times smaller than today's
computers.
ADVANTAGE OF DNA OVER SILICON
• Cellular supplies of DNA make it a cheap resource.
• Made very cleanly, Many times smaller than silicon.
• One pound DNA capacity is too high, Parallel
processing
• Computing speed of One teardrop speed is most
powerful
• 10 trillion DNA molecules can fit into 1 cubic
centimeter, able to hold 10 terabyte of data and
perform 10 trillion calculations at a time.
DISADVANTAGES
• Each stage of parallel operations requires time
measured in hours or days, with extensive human or
mechanical intervention between steps.
• Generating solution sets, even for some relatively
simple problems, may require impractically large
amounts of memory.
• Many empirical uncertainties, including those
involving: actual error rates, the generation of
optimal encoding techniques, and the ability to
perform necessary bio-operations conveniently in
vitro or in vivo.
FUTURE
• Future is very bright to solving complex problem.
• If research gets successful, it will eliminate the
silicon based super computers.
• More powerful DNA computers are likely to be
introduced very soon
BIBLIOGRAPH
• www.dna2z.com.
• www.abcNEWS.com
• www.Howstuffworks.com.
• www.Bio-ITWorld.com
 • www.sciencedaily.com

CONCLUSION: DNA computers will become more common

for solving very complex problems; Just as DNA cloning and
sequencing were once manual tasks, DNA computers will also

become automated. Studying DNA computers may also lead

us to a better future enhancement. With so many possible
advantages over conventional techniques; DNA computing
has great potential for practical use. Future work in this field
should begin to incorporate cost-benefit analysis so the
comparisons can be more appropriately made with existing
techniques and so thwt increased funding can be obtained for
this research that has the potential to benefit many circles of
science and Industry.